def __init__(self,
cache_dirname=None,
MongoDB=None,
replicaSet=None,
db=None,
collection_str='metabolites_meta',
verbose=False,
max_entries=float('inf'),
username=None,
password=None,
authSource='admin',
readPreference='nearest'):
self._collection_str = collection_str
self.verbose = verbose
super().__init__(cache_dirname=cache_dirname,
MongoDB=MongoDB,
replicaSet=replicaSet,
db=db,
verbose=verbose,
max_entries=max_entries,
username=username,
password=password,
authSource=authSource,
readPreference=readPreference)
self._collection = self.client.get_database(
"datanator-test")[collection_str]
self.e_client, self.e_db_obj, self.e_collection = self.con_db('ecmdb')
self.y_client, self.y_db_obj, self.y_collection = self.con_db('ymdb')
self.file_manager = file_util.FileUtil()
self.chem_manager = chem_util.ChemUtil()
self.collation = Collation(locale='en',
strength=CollationStrength.SECONDARY)
def __init__(self,
cache_dirname=None,
collection_str='taxon_tree',
verbose=False,
max_entries=float('inf'),
username=None,
MongoDB=None,
password=None,
db='datanator-test',
authSource='admin',
readPreference='nearest',
replicaSet=None):
self.collection_str = collection_str
super().__init__(cache_dirname=cache_dirname,
MongoDB=MongoDB,
db=db,
verbose=verbose,
max_entries=max_entries,
username=username,
password=password,
authSource=authSource,
readPreference=readPreference,
replicaSet=replicaSet)
self.pipeline_manager = pipelines.Pipeline()
self.chem_manager = chem_util.ChemUtil()
self.file_manager = file_util.FileUtil()
self.collection = self.db_obj[self.collection_str]
self.collation = Collation(locale='en',
strength=CollationStrength.SECONDARY)
def __init__(self, username=None, password=None, server=None, authSource='admin',
database='datanator', max_entries=float('inf'), verbose=True, collection_str='sabio_compound',
readPreference='nearest', replicaSet=None):
super().__init__(MongoDB=server,
db=database,
verbose=verbose, max_entries=max_entries, username=username,
password=password, authSource=authSource, readPreference=readPreference,
replicaSet=replicaSet)
self.file_manager = file_util.FileUtil()
self.max_entries = max_entries
self.verbose = verbose
self.db = self.db_obj
self.collection = self.db[collection_str]
self.collation = Collation(locale='en', strength=CollationStrength.SECONDARY)
self.collection_str = collection_str
def setUpClass(cls):
cls.cache_dirname = tempfile.mkdtemp()
cls.db = 'datanator'
conf = config.TestConfig()
username = conf.USERNAME
password = conf.PASSWORD
MongoDB = conf.SERVER
cls.MongoDB = MongoDB
cls.username = username
cls.password = password
cls.src = query_kegg_orthology.QueryKO(server=cls.MongoDB,
database=cls.db,
verbose=True,
max_entries=20,
username=cls.username,
password=cls.password)
cls.file_manager = file_util.FileUtil()
def __init__(self, username=None, password=None, server=None, authSource='admin',
src_database='datanator', max_entries=float('inf'), verbose=True,
collection='sabio_reaction_entries', destination_database='datanator', cache_dir=None):
'''
Args:
src_database (:obj: `str`): name of database in which source collections reside
destination_database (:obj: `str`): name of database to put the aggregated collection
'''
super().__init__(MongoDB=server, db=destination_database, username=username, password=password,
authSource=authSource)
self.col = self.db_obj[collection]
self.query_manager = query_sabiork_old.QuerySabioOld(MongoDB=server, password=password, authSource=authSource, username=username)
self.metabolites_meta_manager = self.client[src_database]['metabolites_meta']
self.file_manager = file_util.FileUtil()
self.collation = Collation(locale='en', strength=CollationStrength.SECONDARY)
self.verbose = verbose
self.max_entries = max_entries
def __init__(self,
cache_dirname=None,
MongoDB=None,
replicaSet=None,
db='datanator',
collection_str='sabio_rk_old',
verbose=False,
max_entries=float('inf'),
username=None,
password=None,
authSource='admin',
readPreference='nearest'):
self.max_entries = max_entries
super().__init__(cache_dirname=cache_dirname,
MongoDB=MongoDB,
replicaSet=replicaSet,
db=db,
verbose=verbose,
max_entries=max_entries,
username=username,
password=password,
authSource=authSource,
readPreference=readPreference)
self.u = self.client["datanator-test"]["uniprot"]
self.chem_manager = chem_util.ChemUtil()
self.file_manager = file_util.FileUtil()
self.collection = self.db_obj[collection_str]
self.collection_str = collection_str
self.taxon_manager = query_taxon_tree.QueryTaxonTree(
username=username,
password=password,
authSource=authSource,
readPreference=readPreference,
MongoDB=MongoDB,
replicaSet=replicaSet)
self.compound_manager = query_sabio_compound.QuerySabioCompound(
server=MongoDB,
database=db,
username=username,
password=password,
readPreference=readPreference,
authSource=authSource,
replicaSet=replicaSet)
self.collation = Collation(locale='en',
strength=CollationStrength.SECONDARY)
def __init__(self,
cache_dirname=None,
MongoDB=None,
replicaSet=None,
db='datanator',
collection_str='pax',
verbose=False,
max_entries=float('inf'),
username=None,
password=None,
authSource='admin',
readPreference='nearest'):
"""Instantiating query_pax
Args:
cache_dirname (str, optional): temparory cache director. Defaults to None.
MongoDB (str, optional): mongodb server address. Defaults to None.
replicaSet (str, optional): name of mongodb replicaset. Defaults to None.
db (str, optional): name of database in which pax collection resides. Defaults to 'datanator'.
collection_str (str, optional): name of collection. Defaults to 'pax'.
verbose (bool, optional): display verbose messages. Defaults to False.
max_entries (float, optional): max number of operations, mainly used for tests. Defaults to float('inf').
username (str, optional): db authentication username. Defaults to None.
password (str, optional): db authentication password. Defaults to None.
authSource (str, optional): authentication database. Defaults to 'admin'.
readPreference (str, optional): mongodb readpreference. Defaults to 'primary'.
"""
super().__init__(cache_dirname=cache_dirname,
MongoDB=MongoDB,
replicaSet=replicaSet,
db=db,
verbose=verbose,
max_entries=max_entries,
username=username,
password=password,
authSource=authSource,
readPreference=readPreference)
self.collation = Collation(locale='en',
strength=CollationStrength.SECONDARY)
self.chem_manager = chem_util.ChemUtil()
self.file_manager = file_util.FileUtil()
self.max_entries = max_entries
self.verbose = verbose
self.collection = self.db_obj[collection_str]
def __init__(self,
username=None,
password=None,
server=None,
authSource='admin',
database='datanator',
max_entries=float('inf'),
verbose=True,
collection_str='uniprot',
readPreference='nearest',
replicaSet=None):
super().__init__(MongoDB=server,
username=username,
password=password,
authSource=authSource,
db=database,
readPreference=readPreference,
replicaSet=replicaSet)
self.taxon_manager = query_taxon_tree.QueryTaxonTree(
MongoDB=server,
username=username,
password=password,
authSource=authSource,
db=database,
replicaSet=replicaSet)
self.taxon_col = self.db_obj['taxon_tree']
self.kegg_manager = query_kegg_orthology.QueryKO(username=username,
password=password,
server=server,
authSource=authSource,
replicaSet=replicaSet)
self.file_manager = file_util.FileUtil()
self.max_entries = max_entries
self.verbose = verbose
self.collection = self.db_obj[collection_str]
self.paxdb_collection = self.db_obj['pax']
self.collation = Collation(locale='en',
strength=CollationStrength.SECONDARY)
self.collection_str = collection_str
def __init__(self,
MongoDB=None,
db=None,
collection_str=None,
username=None,
password=None,
authSource='admin',
readPreference='nearest',
verbose=True,
replicaSet=None):
super().__init__(MongoDB=MongoDB,
db=db,
verbose=verbose,
username=username,
password=password,
authSource=authSource,
readPreference=readPreference,
replicaSet=replicaSet)
self.file_manager = file_util.FileUtil()
self._collection = self.db_obj[collection_str]
self.collation = Collation(locale='en',
strength=CollationStrength.SECONDARY)
def __init__(self,
cache_dirname=None,
MongoDB=None,
replicaSet=None,
db='datanator',
collection_str='sabio_rk',
verbose=False,
max_entries=float('inf'),
username=None,
password=None,
authSource='admin'):
self.max_entries = max_entries
super().__init__(cache_dirname=cache_dirname,
MongoDB=MongoDB,
replicaSet=replicaSet,
db=db,
verbose=verbose,
max_entries=max_entries,
username=username,
password=password,
authSource=authSource)
self.chem_manager = chem_util.ChemUtil()
self.file_manager = file_util.FileUtil()
self.collection = self.db_obj[collection_str]
def setUpClass(cls):
cls.cache_dirname = tempfile.mkdtemp()
cls.src = file_util.FileUtil()